Trees
Gökce Ergün
2/3/2021
Hello world
Libraries that are used
#install.packages('dplyr')
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union#install.packages('lubridate')
library(lubridate)##
## Attaching package: 'lubridate'## The following objects are masked from 'package:base':
##
## date, intersect, setdiff, union#install.packages('tidyr')
library(tidyr)
#install.packages('ggplot2')
library(ggplot2)
library(tidyverse)## -- Attaching packages --------------------------------------- tidyverse 1.3.0 --## v tibble 3.0.5 v stringr 1.4.0
## v readr 1.4.0 v forcats 0.5.1
## v purrr 0.3.4## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x lubridate::as.difftime() masks base::as.difftime()
## x lubridate::date() masks base::date()
## x dplyr::filter() masks stats::filter()
## x lubridate::intersect() masks base::intersect()
## x dplyr::lag() masks stats::lag()
## x lubridate::setdiff() masks base::setdiff()
## x lubridate::union() masks base::union()#install.packages('gganimate')
library(gganimate)
#install.packages('gifski')
library(gifski)
#install.packages('av')
library(av)
#install.packages('ggmap')
library(ggmap)## Google's Terms of Service: https://cloud.google.com/maps-platform/terms/.## Please cite ggmap if you use it! See citation("ggmap") for details.#install.packages('shiny')
library(shiny)
#install.packages('leaflet')
library(leaflet)Reading the data
df_trees_orig <- read.csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-01-28/sf_trees.csv')We create a copy of data to preserve its original form in case we want to look at it for reference
df_trees <- df_trees_origData Cleaning
We look at the data structure, and see all the string variables are saved as char. We would rather have them as factors for potential modelling use.
str(df_trees)## 'data.frame': 192987 obs. of 12 variables:
## $ tree_id : int 53719 30313 30312 30314 30315 30316 48435 30319 30318 30320 ...
## $ legal_status: chr "Permitted Site" "Permitted Site" "Permitted Site" "DPW Maintained" ...
## $ species : chr "Tree(s) ::" "Tree(s) ::" "Tree(s) ::" "Pittosporum undulatum :: Victorian Box" ...
## $ address : chr "2963 Webster St" "501 Arkansas St" "501 Arkansas St" "501 Arkansas St" ...
## $ site_order : int 1 3 2 1 5 6 4 2 1 3 ...
## $ site_info : chr "Sidewalk: Curb side : Cutout" "Sidewalk: Curb side : Cutout" "Sidewalk: Curb side : Cutout" "Sidewalk: Curb side : Cutout" ...
## $ caretaker : chr "Private" "Private" "Private" "Private" ...
## $ date : chr "1955-09-19" "1955-10-20" "1955-10-20" "1955-10-20" ...
## $ dbh : int NA NA NA 16 NA NA NA NA NA NA ...
## $ plot_size : chr NA NA NA NA ...
## $ latitude : num 37.8 37.8 37.8 37.8 37.8 ...
## $ longitude : num -122 -122 -122 -122 -122 ...Changing columns with type character to type factor. you need double brackets because single bracket indexing returns a df object, which always evaluates to FALSE. Double brackets returns you the column as a vector whose data type can be tested. Alternatively, we can use single brackets but explicitly calling all rows and columns i.e [,i]
for (i in 1:12){
if (is.character(df_trees[,i]) == TRUE) {
df_trees[,i]<-as.factor(df_trees[,i])
}
}date column has char data type. We change it to date.
# df_trees$date <- as.Date(df_trees$date,format="%Y-%m-%d") #using base r
df_trees$date <- lubridate::ymd(df_trees$date) #using lubridatesave the planted year of the tree as a separate column
# df_trees$year <- format(df_trees$date, "%Y") #using base r
df_trees$year <- year(df_trees$date) # using lubridate
class(df_trees$year)## [1] "numeric"take a look at the format of species name in species column.
head(unique(df_trees$species))## [1] Tree(s) ::
## [2] Pittosporum undulatum :: Victorian Box
## [3] Acacia melanoxylon :: Blackwood Acacia
## [4] Magnolia grandiflora :: Southern Magnolia
## [5] Corymbia ficifolia :: Red Flowering Gum
## [6] Ginkgo biloba :: Maidenhair Tree
## 571 Levels: :: ... Ziziphus jujuba :: Jujubewe see that for each species, the species column reports both the latin and common names. For future analysis, it might be more convenient to split the latin and common names into respective columns.
Separate the species column into latin and common name columns.
df_trees <- df_trees %>%
separate(species, sep = "::", remove = FALSE, into = c('species_lat', 'species_nor'))Check the percentage of missing values in each column
for (col in colnames(df_trees)){
print(paste(col, "=", mean(is.na(df_trees[[col]])))) #mean takes percentage here because adds up all TRUES (since their value is 1)
#and divides by total number of values (TRUE + FALSE)
}## [1] "tree_id = 0"
## [1] "legal_status = 0.000279811593527025"
## [1] "species = 0"
## [1] "species_lat = 0"
## [1] "species_nor = 0"
## [1] "address = 0.00770518221434604"
## [1] "site_order = 0.00846689155228072"
## [1] "site_info = 0"
## [1] "caretaker = 0"
## [1] "date = 0.645691160544493"
## [1] "dbh = 0.216693352401975"
## [1] "plot_size = 0.259152170871613"
## [1] "latitude = 0.0146745635716395"
## [1] "longitude = 0.0146745635716395"
## [1] "year = 0.645691160544493"Column with most significant amount of missing data is the date column.
We see almost every species has missing values (517 out of 571 species) so there is at least no clear indication that the data is missing not at random.
df_trees %>% filter(is.na(date))%>%
select(species)%>%
unique() %>% dim()## [1] 517 1further analysis of missing date values: percentage of observations with missing date values, per species.
df_trees_datena <- df_trees %>% filter(is.na(date)) %>%
count(species)
df_trees_species_count <- df_trees %>% count(species)
df_trees_merge <- dplyr::left_join(df_trees_species_count, df_trees_datena, by="species", suffix = c("total", "date.na"))
df_trees_merge$percent.missing <- df_trees_merge$ndate.na / df_trees_merge$ntotal
df_trees_merge %>%
arrange(desc(ntotal), desc(percent.missing))## species
## 1 Tree(s) ::
## 2 Platanus x hispanica :: Sycamore: London Plane
## 3 Metrosideros excelsa :: New Zealand Xmas Tree
## 4 Lophostemon confertus :: Brisbane Box
## 5 Tristaniopsis laurina :: Swamp Myrtle
## 6 Pittosporum undulatum :: Victorian Box
## 7 Prunus cerasifera :: Cherry Plum
## 8 Magnolia grandiflora :: Southern Magnolia
## 9 Arbutus 'Marina' :: Hybrid Strawberry Tree
## 10 Ficus microcarpa nitida 'Green Gem' :: Indian Laurel Fig Tree 'Green Gem'
## 11 Prunus serrulata 'Kwanzan' :: Kwanzan Flowering Cherry
## 12 Acacia melanoxylon :: Blackwood Acacia
## 13 Maytenus boaria :: Mayten
## 14 Olea europaea :: Olive Tree
## 15 Corymbia ficifolia :: Red Flowering Gum
## 16 Callistemon citrinus :: Lemon Bottlebrush
## 17 Ginkgo biloba :: Maidenhair Tree
## 18 Pyrus calleryana :: Ornamental Pear
## 19 Prunus serrulata :: Ornamental Cherry
## 20 Eriobotrya deflexa :: Bronze Loquat
## 21 Ulmus parvifolia :: Chinese Elm
## 22 Pinus radiata :: Monterey Pine
## 23 Ligustrum lucidum :: Glossy Privet
## 24 Pyrus kawakamii :: Evergreen Pear
## 25 Cupressus macrocarpa :: Monterey Cypress
## 26 ::
## 27 Tristaniopsis laurina 'Elegant' :: Small-leaf Tristania 'Elegant'
## 28 Pittosporum crassifolium :: Karo Tree
## 29 Melaleuca quinquenervia :: Cajeput
## 30 Cordyline australis :: Dracena Palm
## 31 Ficus nitida :: Laurel Fig
## 32 Myoporum laetum :: Myoporum
## 33 Liquidambar styraciflua :: American Sweet Gum
## 34 Juniperus chinensis :: Juniper
## 35 Ficus retusa nitida :: Banyan Fig
## 36 Tristania conferta ::
## 37 Jacaranda mimosifolia :: Jacaranda
## 38 Lagunaria patersonii :: Primrose Tree
## 39 Schinus terebinthifolius :: Brazilian Pepper
## 40 Eucalyptus polyanthemos :: Silver Dollar Eucalyptus
## 41 Washingtonia robusta :: Mexican Fan Palm
## 42 Ficus microcarpa :: Chinese Banyan
## 43 Callistemon viminalis :: Weeping Bottlebrush
## 44 Magnolia grandiflora 'Little Gem' :: Little Gem Magnolia
## 45 Agonis flexuosa :: Peppermint Willow
## 46 Phoenix canariensis :: Canary Island Date Palm
## 47 Acer rubrum :: Red Maple
## 48 Syagrus romanzoffianum :: Queen Palm
## 49 Ceratonia siliqua :: Carob
## 50 Laurus nobilis :: Sweet Bay: Grecian Laurel
## 51 Acacia baileyana :: Bailey's Acacia
## 52 Rhaphiolepis Majestic Beauty :: Indian Hawthorn 'Majestic Beau'
## 53 Eucalyptus sideroxylon :: Red Ironbark
## 54 Crataegus phaenopyrum :: Washington Hawthorn
## 55 Afrocarpus gracilior :: Fern Pine
## 56 Arbutus unedo :: Strawberry Tree
## 57 Rhamnus alaternus :: Italian Buckthorn
## 58 Quercus agrifolia :: Coast Live Oak
## 59 Pyrus calleryana 'Aristocrat' :: Aristocrat Callery Pear
## 60 Fraxinus uhdei :: Shamel Ash: Evergreen Ash
## 61 Eucalyptus Spp :: Eucalyptus
## 62 Lyonothamnus floribundus subsp. asplenifolius :: Santa Cruz Ironwood
## 63 Leptospermum scoparium :: New Zealand Tea Tree
## 64 Eucalyptus globulus :: Blue Gum
## 65 Crataegus laevigata :: English Hawthorn
## 66 Syzygium paniculatum :: Brush Cherry
## 67 Geijera parviflora :: Australian Willow
## 68 Platanus x hispanica 'Yarwood' :: Yarwood Sycamore
## 69 Ulmus pumila :: Siberian Elm
## 70 Pinus pinea :: Italian Stone Pine
## 71 Pistacia chinensis :: Chinese Pistache
## 72 Trachycarpus fortunei :: Windmill Palm
## 73 Acer palmatum :: Japanese Maple
## 74 Leptospermum laevigatum :: Australian Tea Tree
## 75 Dodonaea viscosa :: Hop Bush
## 76 Acer buergeranum :: Trident Maple
## 77 Pinus canariensis :: Canary Island Pine
## 78 Yucca gloriosa :: Spanish Dagger
## 79 Magnolia grandiflora 'Samuel Sommer' :: Samuel Sommer Magnolia
## 80 Taxus baccata :: Irish Yew
## 81 Dodonaea viscosa 'Purpurea' :: Purple Hopseed Bush
## 82 Melaleuca linariifolia :: Flaxleaf Paperbark
## 83 Schinus molle :: California Pepper
## 84 Sequoia sempervirens :: Coast Redwood
## 85 Fraxinus spp :: Ash Spp
## 86 Photinia fraseri :: Photinia: Chinese photinia
## 87 Populus nigra 'Italica' :: Lombardy Poplar
## 88 Acacia stenophylla :: Shoestring Acacia
## 89 Liriodendron tulipifera :: Tulip Tree
## 90 Ceanothus 'Ray Hartman' :: California Lilac 'Ray Hartman'
## 91 Pittosporum tenuifolium :: Tawhiwhi Pittosporum
## 92 Prunus blireiana :: Flowering Plum
## 93 Magnolia grandiflora 'Saint Mary' :: Saint Mary Magnolia
## 94 Ulmus americana :: American Elm
## 95 Fraxinus oxycarpa 'Raywood' :: Raywood Ash
## 96 Prunus x yedoensis :: Yoshino Cherry
## 97 Prunus cerasifera 'Krauter vesuvius' :: Purple Leaf Plum Krauter Vesuvius
## 98 Koelreuteria paniculata :: Golden Rain Tree
## 99 Melaleuca ericifolia :: Heath Melaleuca
## 100 Pinus Spp :: Pine Spp
## 101 Cupaniopsis anacardioides :: Carrotwood
## 102 Olea europaea 'Fruitless' :: Fruitless Olive
## 103 Quercus suber :: Cork Oak
## 104 Magnolia doltsopa :: Himalayan Magnolia
## 105 Podocarpus macrophyllus :: Yew Pine
## 106 Podocarpus gracilor :: Fern Pine
## 107 Celtis sinensis :: Chinese Hackberry
## 108 Robinia x ambigua 'Purple Robe' :: Purple Robe Locust
## 109 Chamaerops humilis :: Mediterranean Fan Palm
## 110 Pyrus calleryana 'Chanticleer' :: Ornamental Pear Tree 'Chanticleer'
## 111 Eucalyptus nicholii :: Nichol's Willow-Leafed Peppermint
## 112 Ulmus spp :: Elm Spp
## 113 Prunus domestica 'Mariposa' :: Mariposa Plum
## 114 Eriobotrya japonica :: Edible Loquat
## 115 Acacia longifolia :: Golden Wattle
## 116 Cupressus sempervirens :: Italian Cypress
## 117 Pyrus calleryana 'Bradford' :: Ornamental Pear: Bradford
## 118 Ligustrum japonicum :: Japanese Privet
## 119 Betula pendula :: European White Birch
## 120 Cotoneaster SPP :: Cotoneaster
## 121 Acer x freemanii :: Freeman Maple
## 122 Ginkgo biloba 'Autumn Gold' :: Ginkgo: Autumn Gold
## 123 Agonis flexuosa 'After Dark' :: Peppermint willow 'After Dark'
## 124 Cedrus deodara :: Deodar Cedar
## 125 Prunus spp :: Cherry
## 126 Ulmus parvifolia 'Drake' :: Drake's Chinese Elm
## 127 Tilia cordata :: Littleleaf Linden
## 128 Cupressocyparis leylandii :: Leyland Cypress
## 129 Pittosporum eugenioides :: Tarata
## 130 Magnolia grandiflora 'Russet' :: Russet Magnolia
## 131 Thuja occidentalis 'Emerald' :: Emerald Arborvitae
## 132 Melaleuca nesophila :: Pink Melaleuca
## 133 Citrus spp :: Lemon: Orange: Lime
## 134 Quercus ilex :: Holly Oak
## 135 Malus floribunda :: Showy Crab Apple: Japanese Crabapple
## 136 Ceanothus Sps :: California lilac
## 137 Hymenosporum flavum :: Sweet Shade
## 138 Cinnamomum camphora :: Camphor Tree
## 139 Photinia fraseri :: Photinia Tree
## 140 Prunus cerasifera 'Atropurpurea' :: Purple-Leaf Plum
## 141 Leptospermum scoparium 'Ruby Glow' :: New Zealand Ruby Glow Tea Tree
## 142 Arecastrum romanzoffianum :: Queen Palm
## 143 Olea europaea 'Wilsonii' :: Wilson Olive Semi-fruitless
## 144 Malus :: Crab Apple
## 145 Robinia x ambigua :: Locust
## 146 Shrub :: Shrub
## 147 Aesculus x carnea :: Red Horse Chestnut
## 148 Brahea edulis :: Guadalupe Palm
## 149 Acacia spp :: Acacia Spp
## 150 Acer rubrum 'Red Sunset' :: Red Swamp Maple
## 151 Pinus thunbergii :: Japanese Black Pine
## 152 Pittosporum tobira :: Japanese Mockorange
## 153 Platanus x hispanica 'Columbia' :: Columbia Hybrid Plane Tree
## 154 Syzygium australe :: Eugenia
## 155 Fraxinus oxycarpa :: Ash
## 156 Lagerstroemia indica :: Crape Myrtle
## 157 Gleditsia triacanthos :: Honey Locust
## 158 Rhaphiolepis indica :: India Hawthorn
## 159 Corymbia maculata :: Spotted Gum
## 160 Grevillea robusta :: Silk Oak Tree
## 161 Melaleuca styphelliodes :: Paperbark Tree
## 162 Morus alba :: White Mulberry
## 163 Eucalyptus lehmanni :: Bushy Yate
## 164 Magnolia spp :: Magnolia
## 165 Ceiba speciosa :: Silk floss
## 166 Fraxinus americana :: American Ash
## 167 Pyrus spp :: Pear Tree
## 168 Liquidambar orientalis :: Oriental Sweet Gum
## 169 Magnolia champaca :: Champa
## 170 Brugmansia spp :: Angel trumpet
## 171 Hakea suaveolens :: Sweet Hakea Tree
## 172 Eucalyptus camaldulensis :: River Red Gum
## 173 Crateagus spp :: Hawthorn
## 174 Cercis occidentalis :: Western Redbud
## 175 Persea americana :: Avocado
## 176 Pyrus calleryana 'New Bradford' :: New Bradford Pear
## 177 Acer rubrum 'Armstrong' :: Armstrong Red Maple
## 178 Olea Majestic Beauty ::
## 179 Acer saccharinum :: Silver Maple
## 180 Zelkova serrata :: Sawleaf Zelkova
## 181 Betula spp :: Birch
## 182 Ficus Spp. ::
## 183 Magnolia x soulangiana :: Saucer Magnolia
## 184 Elaeocarpus decipiens :: Japanese Blueberry Tree
## 185 Carpinus betulus :: European Hornbeam
## 186 Platanus racemosa :: California Sycamore
## 187 Aesculus californica :: California Buckeye
## 188 Liquidambar styraciflua 'Rotundiloba' :: Roundleaf sweetgum
## 189 Heteromeles arbutifolia :: Toyon
## 190 Potential Site :: Potential Site
## 191 Albizia julibrissin :: Mimosa Silk Tree
## 192 Quercus virginiana :: Southern Live Oak
## 193 Ilex aquifolium :: European Holly
## 194 Ilex spp :: Holly Species
## 195 Araucaria heterophylla :: Norfolk Island Pine
## 196 Pittosporum spp :: Pittosporum spp
## 197 Phoenix dactylifera :: Date Palm
## 198 Ilex altaclarensis 'Wilsonii' :: Wilson Holly Tree
## 199 Calocedrus decurrens :: Incense Cedar
## 200 Cedrus atlantica :: Atlas Cedar
## 201 Casuarina cunninghamiana :: Horsetail pine
## 202 Melaleuca spp :: Melaleuca spp
## 203 Olea europaea 'Majestic Beauty' :: Majestic Beauty Fruitless Olive
## 204 Tibochina urvilleana :: Princess Flower
## 205 Prunus persica :: Peach
## 206 Eriobotrya deflexa 'Coppertone' :: Coppertone Loquat
## 207 Ficus carica :: Edible Fig
## 208 Alnus rhombifolia :: White Alder
## 209 Azara microphylla :: Little-Leaf Azara
## 210 Leptospermum scoparium 'Helene Strybing' :: Helene Strybing New Zealand Tea Tree
## 211 Washingtonia filifera :: California Fan Palm
## 212 Magnolia grandiflora 'Majestic Beauty' :: Majestic Beauty Magnolia
## 213 Cercis canadensis :: Eastern Redbud
## 214 Laurus x 'Saratoga' :: Hybrid Laurel
## 215 Palm (unknown Genus) :: Palm Spp
## 216 Eucalyptus leucoxylon mac 'Rosea' :: Yellow Gum
## 217 Koelreuteria bipinnata :: Chinese Flame Tree
## 218 Dracaena draco :: Dragon Tree
## 219 Acacia decurrens :: Acacia: Silver Wattle
## 220 Ulmus 'Prospector' :: Prospector Elm
## 221 Ginkgo biloba 'Fairmont' :: Fairmont Ginkgo
## 222 Yucca elephantipes :: Giant Yucca
## 223 Nerium oleander :: Oleander
## 224 Cassia leptophylla :: Gold Medallion Tree
## 225 Fraxinus americana 'Autumn Purple' :: American Autumn Purple Ash
## 226 Araucaria columnaris :: Coral reef araucaria
## 227 Prunus lyonii :: Catalina Cherry
## 228 Acer rubrum 'October Glory' :: Red October Glory Maple
## 229 Ginkgo biloba 'Princeton Sentry' :: Princeton Sentry Maidenhair
## 230 Ficus rubiginosa :: Port Jackson Fig
## 231 Prunus laurocerasus :: English laurel
## 232 Prunus spp :: Flowering Plum
## 233 Pyracantha 'Santa Cruz' :: Firethorn Tree 'Santa Cruz'
## 234 Acer macrophyllum :: Big Leaf Maple
## 235 Prunus subhirtella 'Pendula' :: Weeping Cherry
## 236 Populus spp :: Poplar Spp
## 237 Casurina stricta :: Beefwood: Drooping She-Oak
## 238 Prunus caroliniana :: Carolina Cherry Laurel
## 239 Corymbia citriodora :: Lemon Scented Gum
## 240 Picea Spp :: Spruce Spp
## 241 Acer palmatum 'Bloodgood' :: Bloodgood Japanese Maple
## 242 Celtis occidentalis :: Common Hackberry
## 243 Acer japonicum :: Japanese Maple
## 244 Pseudotsuga menziesii :: Douglas Fir
## 245 Robinia pseudoacacia :: Black Locust
## 246 Salix spp :: Willow
## 247 Acer spp :: Maple
## 248 Acacia cognata :: River Wattle
## 249 Pinus halepensis :: Allepo Pine
## 250 Ficus macrophylla :: Morton Bay Fig
## 251 Eucalyptus viminalis :: Manna Gum
## 252 Prunus armeniaca :: Apricot
## 253 Acacia baileyana 'Purpurea' :: Purple-leaf Acacia
## 254 Quercus rubra :: Red Oak
## 255 Prunus x yedoensis 'Akebono' :: Daybreak Yoshino Cherry
## 256 Cercis canadensis 'Forest Pansy' :: Forest Pansy Redbud
## 257 Magnolia grandiflora 'D.D. Blanchard' :: D.D. Blanchard Southern Magnolia
## 258 Eucalyptus pulverulenta :: Silver Mountain Gum Tree
## 259 Prunus ilicifoia :: Holly-leaved Cherry
## 260 Bambusa spp :: Bamboo Species
## 261 Nyssa sylvatica :: Tupelo: Sour Gum
## 262 Alnus cordata :: Italian Alder
## 263 Quillaja saponaria :: Chilean Soapbark
## 264 Archontophoenix cunninghamiana :: King Palm
## 265 Celtis australis :: European Hackberry
## 266 Eucalyptus robusta :: Swamp mahogany
## 267 Fremontodendron spp :: Flannel Bush Tree
## 268 Quercus spp :: Oak
## 269 Ulmus carpinifolia 'Frontier' :: Frontier Elm 'Frontier'
## 270 Pinus muricata :: Bishop Pine
## 271 Fagus sylvatica :: European Beech
## 272 Fraxinus x Moraine :: Moraine Ash
## 273 Dicksonia antarctica :: Soft Tree Fern
## 274 Umbellularia californica :: California Bay
## 275 Cussonia spicata :: Cabbage tree
## 276 Podocarpus henkelii :: Long-Leafed Yellow-Wood
## 277 Betula nigra :: River Birch
## 278 Ficus laurel ::
## 279 Quercus lobata :: Valley Oak
## 280 Aesculus x carnea 'Briotii' :: Ruby Horse Chestnut
## 281 Quercus coccinea :: Scarlet Oak
## 282 Pyrus calleryana 'Redspire' :: Ornamental Pear Tree 'Redspire'
## 283 Salix babylonica :: Weeping Willow
## 284 Platanus x hispanica 'Bloodgood' :: Bloodgood London Plane
## 285 Private shrub :: Private Shrub
## 286 Styphnolobium japonicum :: Chinese scholar tree
## 287 Rhus lancea :: African Sumac
## 288 Persea indica :: Indian Bay
## 289 Salix matsudana 'Tortuosa' :: Corkscrew Willow
## 290 Chitalpa tashkentensis ::
## 291 Acacia cyclops :: Cyclops wattle
## 292 Ligustrum ovalifolium :: California privet
## 293 Araucaria araucana :: Monkey puzzle
## 294 Cotinus coggygria 'Royal Purple' :: Smoke tree
## 295 Prunus serrulata 'Akebono' :: 'Akebono' Cherry
## 296 Privet ::
## 297 Metasequoia glyplostroboides :: Dawn Redwood
## 298 Eucalyptus microtheca :: Flooded Box: Coolibah
## 299 Populus tremuloides :: Quaking aspen
## 300 Salix lasiolepis :: Arroyo willow
## 301 Banksia integrifolia :: Coast Banksia
## 302 Prunus amygdalus :: Almond
## 303 Citrus × meyeri 'Improved' :: Improved Meyer Lemon
## 304 Brachychiton populneus :: Bottle Tree
## 305 Hymenosporum flavum :: Sweetshade
## 306 Quercus tomentella :: Island oak
## 307 Ginkgo biloba 'Saratoga' :: Ginkgo: Saratoga
## 308 Ulmus parvifolia 'Sempervirens' :: Weeping Chinese Elm
## 309 Albizia distachya :: Plume Albizia Tree
## 310 Eucalyptus melliodora :: Yellow Box
## 311 Musa spp :: Banana
## 312 Sequoiadendron giganteum :: Sierra Redwood
## 313 Aesculus hippocastanum :: White Horsechestnut
## 314 Howea forsteriana :: Kentia Palm
## 315 Olea europaea 'Swan Hill' :: Olive
## 316 Carpinus betulus 'Fastigiata' :: Upright European Hornbeam
## 317 Cornus florida :: Eastern Dogwood
## 318 Liquidambar styraciflua 'Palo Alto' :: Palo Alto Sweet Gum
## 319 Cedrus atlantica Glauca :: Blue Atlas Cedar
## 320 Cryptomeria japonica :: Japanese Cryptomeria
## 321 Cupressus arizonica :: Arizona Cypress
## 322 Fraxinus velutina 'Glabra' :: Arizona Ash
## 323 Juglans regia :: Walnut: English
## 324 Dypsis cabadae :: Cabada palm
## 325 Thuja plicata :: Western Red Cedar
## 326 Eucalyptus cinerea :: Ash-colored Eucalyptus
## 327 Eucalyptus rudis :: Swamp Gum: Flooded Gum
## 328 Tilia americana :: Basswood Linden
## 329 Corymbia calophylla ::
## 330 Vitex lucens :: Puriri tree
## 331 Yucca spp :: Yucca
## 332 Psidium guajava :: Guava tree
## 333 Solanum rantonnetti ::
## 334 Ailanthus altissima :: Tree Of Heaven
## 335 Aloe barberae :: Tree aloe
## 336 Gleditsia triacanthos 'Shademaster' :: Honey Locust 'Shademaster'
## 337 Citrus aurantifolia 'Bearss' :: Seedless Lime
## 338 Quercus robur :: English Oak
## 339 Fraxinus ornus :: Flowering Ash
## 340 Grevillea 'Red Hooks' :: Silk Oak Tree 'Red Hooks'
## 341 Juglans nigra :: Eastern black walnut
## 342 Populus alba :: White Poplar
## 343 Cornus SPP :: Dogwood
## 344 Brachychiton acerifolius :: Australian Flame Tree
## 345 Grevillea spp :: Silkoak species
## 346 Quercus palustris :: Pin Oak
## 347 Griselinia lucida :: Griselinia
## 348 Prunus serrulata 'Mt. Fuji' :: Mt. Fuji Cherry Tree
## 349 Prunus cerasifera 'Thundercloud' :: Purple-Leaf Plum 'Thundercloud'
## 350 Hakea laurina :: Sea Urchin Tree
## 351 Prunus serrulata 'Amanagawa' :: Flowering Cherry Tree 'Amanagawa'
## 352 Malus x 'Callaway' :: White-Flowered Crabapple
## 353 Prunus serrulata 'Royal Burgundy' :: Royal Burgundy Flowering Cherry Tree
## 354 Juniperus californica :: California juniper
## 355 Phoenix roebelenii :: Pigmy Date Palm
## 356 Sophora japonica 'Regent' :: Regent Scholar Tree
## 357 Persea borbonia :: False Avocado
## 358 Prunus spp 'Purpurea' :: Cherry Plum
## 359 Ginkgo biloba 'Autumn Sentinel' :: Autumn Sentinel Ginkgo
## 360 Brahea aramata :: Mexican Blue Palm
## 361 Prunus x 'Amanogawa' :: Flowering Cherry
## 362 Quercus frainetto 'Trump' :: Hungarian Oak
## 363 Ficus microcarpa 'Retusa' :: Pot Belly Fig
## 364 Pyrus calleryana 'Cleveland' :: Ornamental Pear Tree 'Cleveland'
## 365 Taxodium mucronatum :: Montezuma Cypress
## 366 Syringa :: Lilac Tree
## 367 Magnolia x alba :: White Champaca
## 368 Prunus domestica 'Santa Rosa' :: Santa Rosa Plum
## 369 New Zealand Tea Tree :: New Zealand Tea Tree
## 370 Leptospermum petersonii :: Lemon Scented Tea Tree
## 371 Pyrus calleryana 'Capital' :: Ornamental Pear Tree 'Capital'
## 372 Gleditsia triacanthos 'Sunburst' :: Sunburst Honey Locust
## 373 Leptospermum scoparium 'Snow White' :: New Zealand White Tea Tree
## 374 Chamaecyparis species ::
## 375 Chiranthodendron pentadactylon :: Monkey Hand Tree
## 376 Juglans californica :: Walnut: Black (s.calif)
## 377 Salix discolor :: Pussy Willow
## 378 Viburnum odoratissimum var. awabuki :: Sweet viburnum
## 379 Jubaea chilensis :: Chilean Wine Palm
## 380 Phoenix spp :: Date palm (species unknown)
## 381 Punica granatum 'Wonderfu :: Pomegranate Tree 'Wonderful'
## 382 Schefflera species :: Umbrella tree
## 383 Sophora japonica :: Japanese Pagoda
## 384 Archontophoenix myolensis :: Myola palm
## 385 Cornus nuttallii x florida 'Eddie's White Wonder' :: Eddie's White Wonder Dogwood
## 386 Ulmus 'Frontier' :: Frontier Elm
## 387 Auranticarpa rhombifolia :: Queensland Pittosporum
## 388 Fraxinus angustifolia :: Narrow-leaved Ash
## 389 Pinus thunbergii 'Thunderhead' :: Thunderhead Pine
## 390 Abutilon hybridum :: Flowering maple
## 391 Acca sellowiana :: Pineapple Guava Tree
## 392 Acer pseudoplatanus :: Sycamore Maple
## 393 Arctostaphylos manzanita 'Dr Hurd' :: Dr. Hurd Manzanita
## 394 Eucalyptus saligna :: Sidney Blue Gum
## 395 Populus trichocarpa :: Black Cottonwood Poplar
## 396 Rhopalostylis baueri :: Palm
## 397 Acer circinatum :: Vine Maple
## 398 Butia capitata :: Pindo Palm
## 399 Rhamnus californica :: Coffeeberry Tree
## 400 Sapium sebiferum :: Chinese Tallow
## 401 Tilia americana 'Redmond' :: Redmond Linden
## 402 Chionanthus retusa :: Chinese Fringe Tree
## 403 Diospyros kaki :: Persimmon
## 404 Leucodendron argenteum :: Silver Tree
## 405 Quercus wislizenii :: Interior Live Oak
## 406 Fraxinus holotricha :: Holotricha Ash
## 407 Acacia dealbata :: Silver Wattle
## 408 Acer negundo :: Box Elder
## 409 Callistemon 'Jeffers' :: Purple bottlebrush
## 410 Chamaecyparis lawsoniana :: Port Orford Cedar
## 411 Chamaecyparis obtusa :: Hinoki cypress
## 412 Escallonia bifida :: White escallonia
## 413 Eucalyptus macarthuri :: Camden Wollybutt
## 414 Juglans hindsii :: Walnut: Black (n.calif)
## 415 Juniperus silicicola :: Southern red cedar
## 416 Leucadendron 'Gold Strike' :: Yellow conebush
## 417 Melia azerdarach :: Chinaberry
## 418 Pinus coulteri :: Coulter pine
## 419 Prunus lusitanica :: Portugese Cherry Laurel
## 420 Fortunella margarita :: Kumquat
## 421 Garrya elliptica 'Evie' :: Evie Coast Silktassel Tree
## 422 Metrosideros excelsa 'Aurea' ::
## 423 Quercus alba :: White oak
## 424 Quercus engelmannii :: Engelmann oak
## 425 Radermachera sinica :: China Doll Tree
## 426 Sambucus mexicana :: Blue Elderberry
## 427 Tecoma stans :: Trumpet bush
## 428 Caryota maxima 'Himalaya' :: Himalayan Fishtail Palm
## 429 Malus sylvestris :: Apple
## 430 Acer x freemanii 'Autumn Blaze' :: Autumn Blaze Freeman Maple
## 431 Quercus douglasii :: Blue Oak
## 432 Crataegus laevigata 'Paul's Scarlet' :: Paul's Scarlet Hawthorn
## 433 Malus 'Gala' :: Apple Tree 'Gala'
## 434 Malus floribunda 'Prairie Fire' :: Prairie Fire Crabapple Tree
## 435 Populus canadensis :: Canadian Poplar
## 436 Acacia vestita :: Hairy wattle
## 437 Arbutus unedo 'Compacta' :: Dwarf strawberry tree
## 438 Beaucarnea recurvata :: Ponytail palm
## 439 Chorisia speciosa :: Silk Floss Tree
## 440 Eucalyptus longifolia :: Woollybutt
## 441 Fraxinus velutina :: Modesto Ash
## 442 Garrya elliptica 'James Roof' :: James Roof Coast Silktassel Tree
## 443 Leptospermum quinquenervia :: Tea Tree
## 444 Paulownia fortunei :: Dragon tree
## 445 Phoenix reclinata :: Senegal date palm
## 446 Robinia pseudoacacia 'Umbraculifera' :: Globe Locust
## 447 Ziziphus jujuba :: Jujube
## 448 Ilex opaca :: American Holly
## 449 Platanus occidentalis :: American sycamore
## 450 Corynocarpus laevigata :: New Zealand Laurel
## 451 Liquidambar styraciflua 'Festival' :: Festival Sweet Gum
## 452 Magnolia sargentiana 'Robusta' :: Robusta Magnolia
## 453 Prunus serrula :: Birchbark Cherry
## 454 Tilia spp :: Linden
## 455 Ulmus parvifolia 'Athena' :: Chinese Elm 'Athena'
## 456 Aesculus x carnea 'O'Neill' :: O'Neill Red Horse Chestnut
## 457 Magnolia x foggii 'Jack Fogg' :: Jack Fogg Michelia
## 458 Quercus keloggii :: California Black Oak
## 459 Rhamnus alaternus 'John Edwards' :: John Edwards Buckthorn
## 460 Tilia tomentosa :: Silver Linden
## 461 Acacia iteaphylla :: Willow wattle
## 462 Angohpora spp. :: Angophora species
## 463 Arbutus menziesii :: Pacific Madrone
## 464 Brachychiton discolor ::
## 465 Brachychiton rupestris :: Narrow-leaf bottle tree
## 466 Brahea armata :: Blue hesper palm
## 467 Ceanothus thyrsiflorus :: Blueblossom Ceanothus
## 468 Corylus colurna :: Hazel: Turkish
## 469 Cycas revoluta :: Sago palm
## 470 Erythrina caffra :: Coral tree
## 471 Eucalyptus citriodora :: Lemon scented eucalyptus
## 472 Eucalyptus gunnii :: Cider Gum
## 473 Eucalyptus simmondsi :: Simmond's Peppermint
## 474 Eucalyptus torquata :: Coral Gum
## 475 Fraxinus uhdei 'Tomlinson' :: Tomlinson Ash
## 476 Gleditsia triacanthos 'Aurea' :: Honey Locust 'Aurea'
## 477 Lithocarpus densiflorus :: Tan Oak
## 478 Magnolia x soulangiana 'Rustica Rubra' :: Chinese Magnolia
## 479 Meryta sinclairii :: Puka or puke tree
## 480 Morus rubra :: Red mulbeerry
## 481 Pinus contorta :: Shore Pine
## 482 Platanus orientalis :: Eastern Plane Tree
## 483 Prunus serrulata 'Double Pink Weeping' :: Weeping Double Pink Flowering Cherry
## 484 Sambucus species :: Elderberry
## 485 Schinus polygamus :: Chilean pepper tree
## 486 Styrax japonicus :: Japanese Snowdrop Tree
## 487 Xylosma congestum :: Brush holly
## 488 Citrus × limon 'Lisbon' :: Lisbon Lemon Tree
## 489 Eucalyptus odorata :: Peppermint Box
## 490 Lagerstroemia indica 'Natchez' :: Natchez Crape Myrtle
## 491 Paulownia tomentosa :: Empress Tree
## 492 Prunus campanulata :: Taiwan Flowering Cherry
## 493 Ulmus procera :: English Elm
## 494 Acer palmatum 'Sango Kaku' :: Coral Bark Maple
## 495 Acer rubrum 'Autumn Glory' :: Red Maple Tree 'Autumn Glory'
## 496 Ficus carica 'Black Mission' :: Black Mission Fig
## 497 Juglans 'Paradox' :: Paradox Walnut Tree 'Paradox'
## 498 Liquidambar formosana :: Chinese Sweet Gum
## 499 Liquidambar styraciflua 'Burgundy' :: Burgundy Sweet Gum
## 500 Magnolia doltsopa 'Silvercloud' :: Silvercloud Magnolia
## 501 Metrosideros spp ::
## 502 Pyrus pyrifolia '20th Century' :: Asian Pear '20th Century'
## 503 Robinia x ambigua 'Idahoensis' :: Idaho Pink Locust
## 504 Zelkova serrata 'Village Green' :: Village Green Zelkova
## 505 Acer campestre :: Hedge Maple
## 506 Acer platanoides 'Crimson King' :: Norway maple
## 507 Acer platanoides :: Norway Maple
## 508 Acer saccharum :: Sugar Maple
## 509 Aesculus spp :: Horsechestnut
## 510 Alnus rubra :: Red Alder
## 511 Araucaria bidwillii :: Bunya Bunya
## 512 Brahea brandegeei :: San Jose hesper palm
## 513 Callistemon salignus :: White flowering bottlebrush
## 514 Carya illinoensis :: Pecan
## 515 Castanea dentata :: American Chestnut
## 516 Catalpa speciosa :: Northern Catalpa
## 517 Cedrela fissilis :: Argentine cedar
## 518 Cedrus libani :: Lebanon cedar
## 519 Cercocarpus betuloides :: Mountain mahogany
## 520 Crinodendron patagua :: Lily-of-the-Valley Tree
## 521 Cupressus spp :: Cypress species
## 522 Dypsis decaryi :: Triangle palm
## 523 Euphorbia ingens :: Candelabra tree
## 524 Fraxinus velutina 'Modesto' :: Modesto Ash Tree 'Modesto'
## 525 Geijera spp :: Geijera
## 526 Juniperus scopulorum 'Pat :: Juniper Tree 'Pathfinder'
## 527 Lagerstroemia spp :: Crape myrtle species
## 528 Lagerstroemia x 'Tuscarora' :: Tuscarora Crape Myrtle
## 529 Livistona chinensis :: Chinese fan palm
## 530 Macadamia tetraphylla :: Macadamia
## 531 Magnolia grandiflora 'Timeless Beauty' :: Timeless Beauty Southern Magnolia
## 532 Mangifera indica :: Mango
## 533 Melaleuca leucadendron :: Weeping Tea Tree
## 534 Metrosideros robusta :: Northern Rata Tree
## 535 Moringa oleifera :: Drumstick tree
## 536 Phoenix rupicola :: Cliff date palm
## 537 Pinus pinaster :: Maritime Pine
## 538 Pinus strobus :: Eastern white pine
## 539 Pinus sylvestris :: Scots Pine
## 540 Populus deltoides :: Eastern cottonwood
## 541 Prunus domestica 'Green Gage' :: Green Gage Plum
## 542 Prunus persica nectarina :: Flowering Nectarine Tree
## 543 Pseudopanax lessonii :: Five finger
## 544 Rhopalostylis sapida :: Nikau palm
## 545 Rhus typhina :: Staghorn sumac
## 546 Sorbus aucuparia :: European Mountain Ash Tr
## 547 Stenocarpus sinuatus :: Firewheel tree
## 548 Taxodium distichum :: Bald Cypress
## 549 Torreya californica :: California nutmeg
## 550 Ulmus glabra :: Scotch Elm
## 551 Wodyetia bifurcata :: Foxtail palm
## 552 x Chiranthofremontia lenzii :: Hybrid Monkey Hand Tree
## 553 Yucca aloifolia :: Spanish bayonet
## 554 Acer ginnela :: Amur Maple
## 555 Acer paxii :: Evergreen Maple
## 556 Acer tegmentosum :: Manchurian snakebark maple
## 557 Acer x 'Autumn Blaze' :: Hybrid Maple
## 558 Cercidiphyllum japonicum :: Katsura tree
## 559 Citrus x hystrix :: Kaffir lime
## 560 Fagus sylvatica 'Red Obelisk' :: Red Obelisk Beech
## 561 Ficus carica 'Brown Turkey' :: Brown Turkey Fig
## 562 Lagerstroemia indica 'Tuscarora' :: Tuscarora Crape Myrtle
## 563 Liquidambar styraciflua 'Slender Silhoutte' :: Upright Liquidambar
## 564 Malus 'Fuji' :: Fuji Apple Tree 'Fuji'
## 565 Myrica californica :: Pacific Wax Myrtle Tree
## 566 Persea americana 'Stewart' :: Stewart Avocado
## 567 Pinus torreyana :: Torrey Pine
## 568 Prunus sargentii 'Columnaris' :: Sargent Cherry Tree 'Columnaris'
## 569 Prunus sargentii :: Sargent Cherry
## 570 Pyrus pyrifolia 'Sainseiki' :: Asian Pear 'Sainseiki'
## 571 Ulmus parvifolia 'True Green' :: True Green Chinese Elm
## ntotal ndate.na percent.missing
## 1 11629 1563 0.13440537
## 2 11557 9773 0.84563468
## 3 8744 6470 0.73993596
## 4 8581 4481 0.52220021
## 5 7197 3682 0.51160206
## 6 7122 5080 0.71328279
## 7 6716 4130 0.61494937
## 8 6285 3956 0.62943516
## 9 5702 2456 0.43072606
## 10 5624 4882 0.86806543
## 11 4025 2581 0.64124224
## 12 3956 3584 0.90596562
## 13 3899 2495 0.63990767
## 14 3694 2456 0.66486194
## 15 3575 3143 0.87916084
## 16 3266 2651 0.81169626
## 17 3212 1917 0.59682441
## 18 2969 1918 0.64600876
## 19 2696 948 0.35163205
## 20 2402 1120 0.46627810
## 21 2366 1900 0.80304311
## 22 2278 2138 0.93854258
## 23 2185 1715 0.78489703
## 24 1974 1017 0.51519757
## 25 1922 1862 0.96878252
## 26 1839 1618 0.87982599
## 27 1797 660 0.36727880
## 28 1795 1315 0.73259053
## 29 1736 790 0.45506912
## 30 1640 1341 0.81768293
## 31 1632 1360 0.83333333
## 32 1590 1347 0.84716981
## 33 1520 1127 0.74144737
## 34 1404 1347 0.95940171
## 35 1387 1207 0.87022350
## 36 1373 910 0.66278223
## 37 1170 603 0.51538462
## 38 1077 436 0.40482823
## 39 1059 771 0.72804533
## 40 1005 824 0.81990050
## 41 994 676 0.68008048
## 42 966 609 0.63043478
## 43 950 524 0.55157895
## 44 935 407 0.43529412
## 45 913 447 0.48959474
## 46 893 656 0.73460246
## 47 890 537 0.60337079
## 48 859 610 0.71012806
## 49 855 688 0.80467836
## 50 855 546 0.63859649
## 51 834 393 0.47122302
## 52 808 261 0.32301980
## 53 718 643 0.89554318
## 54 708 388 0.54802260
## 55 665 452 0.67969925
## 56 632 403 0.63765823
## 57 618 277 0.44822006
## 58 598 416 0.69565217
## 59 574 227 0.39547038
## 60 557 512 0.91921005
## 61 551 412 0.74773140
## 62 548 300 0.54744526
## 63 504 424 0.84126984
## 64 497 487 0.97987928
## 65 492 310 0.63008130
## 66 489 476 0.97341513
## 67 487 274 0.56262834
## 68 438 139 0.31735160
## 69 429 404 0.94172494
## 70 428 420 0.98130841
## 71 428 235 0.54906542
## 72 421 244 0.57957245
## 73 412 342 0.83009709
## 74 406 243 0.59852217
## 75 400 43 0.10750000
## 76 395 202 0.51139241
## 77 393 315 0.80152672
## 78 390 333 0.85384615
## 79 380 49 0.12894737
## 80 379 347 0.91556728
## 81 368 326 0.88586957
## 82 357 168 0.47058824
## 83 350 250 0.71428571
## 84 341 301 0.88269795
## 85 332 279 0.84036145
## 86 332 247 0.74397590
## 87 329 322 0.97872340
## 88 326 136 0.41717791
## 89 320 245 0.76562500
## 90 314 159 0.50636943
## 91 306 284 0.92810458
## 92 302 171 0.56622517
## 93 296 110 0.37162162
## 94 286 270 0.94405594
## 95 276 191 0.69202899
## 96 268 168 0.62686567
## 97 267 81 0.30337079
## 98 260 167 0.64230769
## 99 258 63 0.24418605
## 100 257 241 0.93774319
## 101 251 149 0.59362550
## 102 249 71 0.28514056
## 103 247 132 0.53441296
## 104 242 113 0.46694215
## 105 226 159 0.70353982
## 106 226 111 0.49115044
## 107 222 122 0.54954955
## 108 218 192 0.88073394
## 109 210 170 0.80952381
## 110 201 122 0.60696517
## 111 200 133 0.66500000
## 112 194 186 0.95876289
## 113 194 183 0.94329897
## 114 183 167 0.91256831
## 115 180 129 0.71666667
## 116 176 153 0.86931818
## 117 171 138 0.80701754
## 118 168 149 0.88690476
## 119 161 127 0.78881988
## 120 160 157 0.98125000
## 121 160 102 0.63750000
## 122 159 5 0.03144654
## 123 155 118 0.76129032
## 124 154 146 0.94805195
## 125 154 108 0.70129870
## 126 154 28 0.18181818
## 127 153 109 0.71241830
## 128 151 147 0.97350993
## 129 147 135 0.91836735
## 130 147 49 0.33333333
## 131 146 141 0.96575342
## 132 144 42 0.29166667
## 133 143 133 0.93006993
## 134 143 77 0.53846154
## 135 142 111 0.78169014
## 136 141 130 0.92198582
## 137 140 8 0.05714286
## 138 139 91 0.65467626
## 139 136 14 0.10294118
## 140 134 110 0.82089552
## 141 131 2 0.01526718
## 142 130 18 0.13846154
## 143 126 7 0.05555556
## 144 121 116 0.95867769
## 145 118 NA NA
## 146 116 91 0.78448276
## 147 116 71 0.61206897
## 148 108 99 0.91666667
## 149 107 106 0.99065421
## 150 106 NA NA
## 151 105 100 0.95238095
## 152 103 92 0.89320388
## 153 103 57 0.55339806
## 154 100 100 1.00000000
## 155 100 73 0.73000000
## 156 99 81 0.81818182
## 157 99 66 0.66666667
## 158 98 72 0.73469388
## 159 97 94 0.96907216
## 160 97 77 0.79381443
## 161 97 63 0.64948454
## 162 94 77 0.81914894
## 163 92 91 0.98913043
## 164 92 36 0.39130435
## 165 91 89 0.97802198
## 166 91 84 0.92307692
## 167 91 58 0.63736264
## 168 90 25 0.27777778
## 169 89 55 0.61797753
## 170 87 84 0.96551724
## 171 86 36 0.41860465
## 172 85 84 0.98823529
## 173 84 51 0.60714286
## 174 82 58 0.70731707
## 175 81 78 0.96296296
## 176 81 36 0.44444444
## 177 81 32 0.39506173
## 178 81 9 0.11111111
## 179 80 72 0.90000000
## 180 80 51 0.63750000
## 181 78 63 0.80769231
## 182 76 69 0.90789474
## 183 76 61 0.80263158
## 184 75 58 0.77333333
## 185 74 67 0.90540541
## 186 74 61 0.82432432
## 187 74 51 0.68918919
## 188 72 58 0.80555556
## 189 67 65 0.97014925
## 190 66 59 0.89393939
## 191 64 37 0.57812500
## 192 61 58 0.95081967
## 193 61 57 0.93442623
## 194 60 58 0.96666667
## 195 60 57 0.95000000
## 196 59 39 0.66101695
## 197 58 54 0.93103448
## 198 58 53 0.91379310
## 199 57 54 0.94736842
## 200 57 54 0.94736842
## 201 57 51 0.89473684
## 202 57 37 0.64912281
## 203 57 5 0.08771930
## 204 55 42 0.76363636
## 205 54 53 0.98148148
## 206 54 36 0.66666667
## 207 53 50 0.94339623
## 208 53 36 0.67924528
## 209 52 37 0.71153846
## 210 51 NA NA
## 211 50 44 0.88000000
## 212 49 12 0.24489796
## 213 47 39 0.82978723
## 214 47 7 0.14893617
## 215 46 27 0.58695652
## 216 45 44 0.97777778
## 217 45 19 0.42222222
## 218 43 14 0.32558140
## 219 42 37 0.88095238
## 220 42 3 0.07142857
## 221 42 2 0.04761905
## 222 41 29 0.70731707
## 223 40 37 0.92500000
## 224 40 12 0.30000000
## 225 40 NA NA
## 226 39 37 0.94871795
## 227 38 29 0.76315789
## 228 38 13 0.34210526
## 229 38 2 0.05263158
## 230 37 35 0.94594595
## 231 37 33 0.89189189
## 232 36 20 0.55555556
## 233 34 34 1.00000000
## 234 34 32 0.94117647
## 235 34 29 0.85294118
## 236 33 30 0.90909091
## 237 33 20 0.60606061
## 238 32 23 0.71875000
## 239 31 31 1.00000000
## 240 31 28 0.90322581
## 241 31 26 0.83870968
## 242 30 27 0.90000000
## 243 30 24 0.80000000
## 244 29 26 0.89655172
## 245 29 26 0.89655172
## 246 29 26 0.89655172
## 247 29 22 0.75862069
## 248 28 20 0.71428571
## 249 27 26 0.96296296
## 250 27 23 0.85185185
## 251 26 26 1.00000000
## 252 26 25 0.96153846
## 253 26 2 0.07692308
## 254 25 17 0.68000000
## 255 24 9 0.37500000
## 256 24 8 0.33333333
## 257 24 3 0.12500000
## 258 23 22 0.95652174
## 259 23 22 0.95652174
## 260 23 21 0.91304348
## 261 23 21 0.91304348
## 262 23 20 0.86956522
## 263 23 19 0.82608696
## 264 23 18 0.78260870
## 265 23 8 0.34782609
## 266 22 20 0.90909091
## 267 22 20 0.90909091
## 268 22 13 0.59090909
## 269 22 10 0.45454545
## 270 21 21 1.00000000
## 271 21 15 0.71428571
## 272 20 18 0.90000000
## 273 20 17 0.85000000
## 274 19 19 1.00000000
## 275 19 18 0.94736842
## 276 19 18 0.94736842
## 277 19 15 0.78947368
## 278 19 13 0.68421053
## 279 19 9 0.47368421
## 280 19 8 0.42105263
## 281 19 1 0.05263158
## 282 18 17 0.94444444
## 283 18 17 0.94444444
## 284 18 7 0.38888889
## 285 17 16 0.94117647
## 286 17 15 0.88235294
## 287 17 14 0.82352941
## 288 17 13 0.76470588
## 289 17 11 0.64705882
## 290 17 7 0.41176471
## 291 16 16 1.00000000
## 292 16 16 1.00000000
## 293 16 14 0.87500000
## 294 16 14 0.87500000
## 295 16 11 0.68750000
## 296 16 10 0.62500000
## 297 15 15 1.00000000
## 298 15 14 0.93333333
## 299 15 14 0.93333333
## 300 15 14 0.93333333
## 301 15 3 0.20000000
## 302 14 11 0.78571429
## 303 14 10 0.71428571
## 304 14 9 0.64285714
## 305 14 8 0.57142857
## 306 14 4 0.28571429
## 307 14 2 0.14285714
## 308 14 1 0.07142857
## 309 13 13 1.00000000
## 310 13 13 1.00000000
## 311 13 13 1.00000000
## 312 13 13 1.00000000
## 313 13 12 0.92307692
## 314 13 10 0.76923077
## 315 13 10 0.76923077
## 316 13 6 0.46153846
## 317 13 5 0.38461538
## 318 13 NA NA
## 319 12 12 1.00000000
## 320 12 12 1.00000000
## 321 12 12 1.00000000
## 322 12 12 1.00000000
## 323 12 12 1.00000000
## 324 12 11 0.91666667
## 325 12 11 0.91666667
## 326 12 10 0.83333333
## 327 12 10 0.83333333
## 328 12 8 0.66666667
## 329 11 11 1.00000000
## 330 11 11 1.00000000
## 331 11 10 0.90909091
## 332 11 9 0.81818182
## 333 11 7 0.63636364
## 334 10 9 0.90000000
## 335 10 9 0.90000000
## 336 10 9 0.90000000
## 337 10 8 0.80000000
## 338 10 5 0.50000000
## 339 10 NA NA
## 340 10 NA NA
## 341 9 9 1.00000000
## 342 9 9 1.00000000
## 343 9 8 0.88888889
## 344 9 7 0.77777778
## 345 9 7 0.77777778
## 346 9 7 0.77777778
## 347 9 4 0.44444444
## 348 9 4 0.44444444
## 349 9 3 0.33333333
## 350 9 1 0.11111111
## 351 9 1 0.11111111
## 352 9 NA NA
## 353 9 NA NA
## 354 8 8 1.00000000
## 355 8 8 1.00000000
## 356 8 8 1.00000000
## 357 8 6 0.75000000
## 358 8 3 0.37500000
## 359 8 1 0.12500000
## 360 8 NA NA
## 361 8 NA NA
## 362 8 NA NA
## 363 7 7 1.00000000
## 364 7 7 1.00000000
## 365 7 7 1.00000000
## 366 7 6 0.85714286
## 367 7 5 0.71428571
## 368 7 5 0.71428571
## 369 7 2 0.28571429
## 370 7 1 0.14285714
## 371 7 1 0.14285714
## 372 7 NA NA
## 373 7 NA NA
## 374 6 6 1.00000000
## 375 6 6 1.00000000
## 376 6 6 1.00000000
## 377 6 6 1.00000000
## 378 6 6 1.00000000
## 379 6 5 0.83333333
## 380 6 5 0.83333333
## 381 6 5 0.83333333
## 382 6 5 0.83333333
## 383 6 5 0.83333333
## 384 6 4 0.66666667
## 385 6 4 0.66666667
## 386 6 4 0.66666667
## 387 6 3 0.50000000
## 388 6 NA NA
## 389 6 NA NA
## 390 5 5 1.00000000
## 391 5 5 1.00000000
## 392 5 5 1.00000000
## 393 5 5 1.00000000
## 394 5 5 1.00000000
## 395 5 5 1.00000000
## 396 5 5 1.00000000
## 397 5 4 0.80000000
## 398 5 4 0.80000000
## 399 5 4 0.80000000
## 400 5 4 0.80000000
## 401 5 4 0.80000000
## 402 5 3 0.60000000
## 403 5 3 0.60000000
## 404 5 2 0.40000000
## 405 5 2 0.40000000
## 406 5 1 0.20000000
## 407 4 4 1.00000000
## 408 4 4 1.00000000
## 409 4 4 1.00000000
## 410 4 4 1.00000000
## 411 4 4 1.00000000
## 412 4 4 1.00000000
## 413 4 4 1.00000000
## 414 4 4 1.00000000
## 415 4 4 1.00000000
## 416 4 4 1.00000000
## 417 4 4 1.00000000
## 418 4 4 1.00000000
## 419 4 4 1.00000000
## 420 4 3 0.75000000
## 421 4 3 0.75000000
## 422 4 3 0.75000000
## 423 4 3 0.75000000
## 424 4 3 0.75000000
## 425 4 3 0.75000000
## 426 4 3 0.75000000
## 427 4 3 0.75000000
## 428 4 2 0.50000000
## 429 4 2 0.50000000
## 430 4 1 0.25000000
## 431 4 1 0.25000000
## 432 4 NA NA
## 433 4 NA NA
## 434 4 NA NA
## 435 4 NA NA
## 436 3 3 1.00000000
## 437 3 3 1.00000000
## 438 3 3 1.00000000
## 439 3 3 1.00000000
## 440 3 3 1.00000000
## 441 3 3 1.00000000
## 442 3 3 1.00000000
## 443 3 3 1.00000000
## 444 3 3 1.00000000
## 445 3 3 1.00000000
## 446 3 3 1.00000000
## 447 3 3 1.00000000
## 448 3 2 0.66666667
## 449 3 2 0.66666667
## 450 3 1 0.33333333
## 451 3 1 0.33333333
## 452 3 1 0.33333333
## 453 3 1 0.33333333
## 454 3 1 0.33333333
## 455 3 1 0.33333333
## 456 3 NA NA
## 457 3 NA NA
## 458 3 NA NA
## 459 3 NA NA
## 460 3 NA NA
## 461 2 2 1.00000000
## 462 2 2 1.00000000
## 463 2 2 1.00000000
## 464 2 2 1.00000000
## 465 2 2 1.00000000
## 466 2 2 1.00000000
## 467 2 2 1.00000000
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## 469 2 2 1.00000000
## 470 2 2 1.00000000
## 471 2 2 1.00000000
## 472 2 2 1.00000000
## 473 2 2 1.00000000
## 474 2 2 1.00000000
## 475 2 2 1.00000000
## 476 2 2 1.00000000
## 477 2 2 1.00000000
## 478 2 2 1.00000000
## 479 2 2 1.00000000
## 480 2 2 1.00000000
## 481 2 2 1.00000000
## 482 2 2 1.00000000
## 483 2 2 1.00000000
## 484 2 2 1.00000000
## 485 2 2 1.00000000
## 486 2 2 1.00000000
## 487 2 2 1.00000000
## 488 2 1 0.50000000
## 489 2 1 0.50000000
## 490 2 1 0.50000000
## 491 2 1 0.50000000
## 492 2 1 0.50000000
## 493 2 1 0.50000000
## 494 2 NA NA
## 495 2 NA NA
## 496 2 NA NA
## 497 2 NA NA
## 498 2 NA NA
## 499 2 NA NA
## 500 2 NA NA
## 501 2 NA NA
## 502 2 NA NA
## 503 2 NA NA
## 504 2 NA NA
## 505 1 1 1.00000000
## 506 1 1 1.00000000
## 507 1 1 1.00000000
## 508 1 1 1.00000000
## 509 1 1 1.00000000
## 510 1 1 1.00000000
## 511 1 1 1.00000000
## 512 1 1 1.00000000
## 513 1 1 1.00000000
## 514 1 1 1.00000000
## 515 1 1 1.00000000
## 516 1 1 1.00000000
## 517 1 1 1.00000000
## 518 1 1 1.00000000
## 519 1 1 1.00000000
## 520 1 1 1.00000000
## 521 1 1 1.00000000
## 522 1 1 1.00000000
## 523 1 1 1.00000000
## 524 1 1 1.00000000
## 525 1 1 1.00000000
## 526 1 1 1.00000000
## 527 1 1 1.00000000
## 528 1 1 1.00000000
## 529 1 1 1.00000000
## 530 1 1 1.00000000
## 531 1 1 1.00000000
## 532 1 1 1.00000000
## 533 1 1 1.00000000
## 534 1 1 1.00000000
## 535 1 1 1.00000000
## 536 1 1 1.00000000
## 537 1 1 1.00000000
## 538 1 1 1.00000000
## 539 1 1 1.00000000
## 540 1 1 1.00000000
## 541 1 1 1.00000000
## 542 1 1 1.00000000
## 543 1 1 1.00000000
## 544 1 1 1.00000000
## 545 1 1 1.00000000
## 546 1 1 1.00000000
## 547 1 1 1.00000000
## 548 1 1 1.00000000
## 549 1 1 1.00000000
## 550 1 1 1.00000000
## 551 1 1 1.00000000
## 552 1 1 1.00000000
## 553 1 1 1.00000000
## 554 1 NA NA
## 555 1 NA NA
## 556 1 NA NA
## 557 1 NA NA
## 558 1 NA NA
## 559 1 NA NA
## 560 1 NA NA
## 561 1 NA NA
## 562 1 NA NA
## 563 1 NA NA
## 564 1 NA NA
## 565 1 NA NA
## 566 1 NA NA
## 567 1 NA NA
## 568 1 NA NA
## 569 1 NA NA
## 570 1 NA NA
## 571 1 NA NAWe look at the total number of observations we would lose if we drop species where missing 100% of date information. And the number is very small relative to total number of observations (n = 192987)
df_trees_merge %>% filter(percent.missing==1) %>% select(ntotal) %>%
sum()## [1] 731 #arrange(desc(percent.missing), desc(ntotal))How the percentage of missing date values per species is distributed. All species that have 100% of date data missing have a very low number of observations (n <=100).
df_trees_merge %>%
ggplot(aes(percent.missing))+geom_histogram() +scale_x_continuous(breaks=seq(0,1, .10))## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.## Warning: Removed 54 rows containing non-finite values (stat_bin).
Therefore, we now filter the cases based on this 100 ntotal threshold to get a cleaner histogram.
df_trees_merge %>% filter(ntotal>100) %>%
ggplot(aes(percent.missing))+geom_histogram() +scale_x_continuous(breaks=seq(0,1, .10))## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.## Warning: Removed 2 rows containing non-finite values (stat_bin).
Exploratory Analysis
Checking year of plantation range. most of the trees (50%) were planted between 2001 and 2020. However, it is likely that many of the older trees simply were not recorded so they either dont appear in our data or have a missing date value.
df_trees %>%
select(year)%>%
quantile(na.rm = TRUE)## 0% 25% 50% 75% 100%
## 1955 1995 2001 2008 2020Create a new column that shows age using the year column to calculate it. Use the more modern approach mutate(). Then use age column to get an overview of the distribution of tree ages via a histogram.
df_trees <- df_trees %>%
mutate(age = year(Sys.Date())-year)
hist(df_trees$age, main = 'Tree Age Distribution', xlab = 'Age', col = 'royalblue2') # using base r
Count the species
df_trees %>%
count(species_lat) %>%
arrange(desc(n)) %>%
top_n(n = 20)## Selecting by n## species_lat n
## 1 Tree(s) 11629
## 2 Platanus x hispanica 11557
## 3 Metrosideros excelsa 8744
## 4 Lophostemon confertus 8581
## 5 Tristaniopsis laurina 7197
## 6 Pittosporum undulatum 7122
## 7 Prunus cerasifera 6716
## 8 Magnolia grandiflora 6285
## 9 Arbutus 'Marina' 5702
## 10 Ficus microcarpa nitida 'Green Gem' 5624
## 11 Prunus serrulata 'Kwanzan' 4025
## 12 Acacia melanoxylon 3956
## 13 Maytenus boaria 3899
## 14 Olea europaea 3694
## 15 Corymbia ficifolia 3575
## 16 Callistemon citrinus 3266
## 17 Ginkgo biloba 3212
## 18 Pyrus calleryana 2969
## 19 Prunus serrulata 2696
## 20 Eriobotrya deflexa 2402Show number of distinct species in a street
df_trees %>%
group_by(address) %>%
summarize(n = n_distinct(species_lat)) %>%
arrange(desc(n))## # A tibble: 85,910 x 2
## address n
## <fct> <int>
## 1 <NA> 43
## 2 900x Carolina St 31
## 3 1201 San Jose Ave 30
## 4 1301 Minnesota St 28
## 5 310 Liberty St 26
## 6 1000 San Jose Ave 24
## 7 1100 San Jose Ave 24
## 8 2200 Sunset Blvd 20
## 9 2600 Sunset Blvd 20
## 10 700 Junipero Serra Blvd 20
## # ... with 85,900 more rowsAnalysis 1: evolution of planted species over time
To do this specific analysis we drop the trees, which have missing date data for obvious reasons. Based on our missing date data analysis in the data cleaning section, we are confident the data does not display any obvious signs of MNAR.
Selected related columns
df_trees_hasdate <- df_trees %>%
filter(!is.na(date)) %>%
select(c("tree_id", "species_lat", "year"))
str(df_trees_hasdate)## 'data.frame': 68377 obs. of 3 variables:
## $ tree_id : int 53719 30313 30312 30314 30315 30316 48435 30319 30318 30320 ...
## $ species_lat: chr "Tree(s) " "Tree(s) " "Tree(s) " "Pittosporum undulatum " ...
## $ year : num 1955 1955 1955 1955 1955 ...df_trees_hasdate$species_lat <- as.factor(df_trees_hasdate$species_lat)
str(df_trees_hasdate)## 'data.frame': 68377 obs. of 3 variables:
## $ tree_id : int 53719 30313 30312 30314 30315 30316 48435 30319 30318 30320 ...
## $ species_lat: Factor w/ 427 levels "","Acacia baileyana ",..: 405 405 405 287 7 7 405 221 221 99 ...
## $ year : num 1955 1955 1955 1955 1955 ...To make the number of species more manageable, we group them by family names (i.e Acacia, Magnolia)
unique(df_trees_hasdate[grep(df_trees_hasdate$species_lat, pattern = "^Acacia", ignore.case = TRUE), 'species_lat'])## [1] Acacia melanoxylon Acacia longifolia
## [3] Acacia stenophylla Acacia baileyana
## [5] Acacia baileyana 'Purpurea' Acacia cognata
## [7] Acacia spp Acacia decurrens
## 427 Levels: Acacia baileyana Acacia baileyana 'Purpurea' ... Zelkova serrata 'Village Green'unique(df_trees_hasdate[grep(df_trees_hasdate$species_lat, pattern = "^Magnolia", ignore.case = TRUE), 'species_lat'])## [1] Magnolia grandiflora
## [2] Magnolia spp
## [3] Magnolia grandiflora 'Little Gem'
## [4] Magnolia champaca
## [5] Magnolia doltsopa
## [6] Magnolia grandiflora 'Samuel Sommer'
## [7] Magnolia grandiflora 'Saint Mary'
## [8] Magnolia grandiflora 'Russet'
## [9] Magnolia x soulangiana
## [10] Magnolia x foggii 'Jack Fogg'
## [11] Magnolia grandiflora 'Majestic Beauty'
## [12] Magnolia grandiflora 'D.D. Blanchard'
## [13] Magnolia sargentiana 'Robusta'
## [14] Magnolia x alba
## [15] Magnolia doltsopa 'Silvercloud'
## 427 Levels: Acacia baileyana Acacia baileyana 'Purpurea' ... Zelkova serrata 'Village Green'It seems that specific species can be grouped together with a general name. Since the general name is the first word of the species name, we will separate the species name into its words and then use the first word as the species general name.
Separate the species_lat column into first and second part
df_trees_hasdate <- df_trees_hasdate %>%
separate(species_lat, sep = " ", remove = FALSE, into = c('species_first', 'species_second', 'species_third'))## Warning: Expected 3 pieces. Additional pieces discarded in 10662 rows [23, 25,
## 87, 88, 89, 91, 92, 93, 94, 97, 104, 105, 106, 111, 113, 119, 120, 121, 129,
## 162, ...].## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 10324 rows [1, 2,
## 3, 7, 17, 20, 30, 31, 33, 36, 38, 39, 41, 42, 43, 45, 46, 47, 48, 50, ...].The code below shows that the number of unique species after recategorizing species_lat is 158.
length(unique(df_trees_hasdate$species_first))## [1] 158Create a count column to save number of planted trees by species, per year.
df_trees_hasdate_tidy <- df_trees_hasdate %>%
group_by(year) %>%
count(species_first) %>%
arrange(year, desc(n)) As a bit of side note we look at the total number of planted trees per year regardless of species to get a sense of overall tree planting
df_trees_hasdate_tidy %>%
select(c('year', 'n')) %>%
aggregate(by = list(df_trees_hasdate_tidy$year), FUN='sum') %>%
ggplot(aes(x = Group.1, y = n)) +
geom_line() +
labs(title = 'Total Number of Planted Trees per Year',
x = 'Year', y = 'Total number of planted trees') +
theme_minimal()
Animated Graph
In this step, We’re going to filter our data set to retain only the top 10 planted species for every given year to keep the visuals understandable. Also we drop the species labelled Tree(s) as this obviously tells us nothing about the species.
df_trees_hasdate_formated <- df_trees_hasdate_tidy %>% subset(species_first != 'Tree(s)') %>%
group_by(year) %>%
mutate(rank = rank(-n)) %>%
filter(rank <=10) In this step, we will create individual static graphs for each year.
staticplot = ggplot(df_trees_hasdate_formated, aes(rank, group = species_first,
fill = as.factor(species_first), color = as.factor(species_first))) +
geom_tile(aes(y = n/2,
height = n,
width = 0.9), alpha = 0.8, color = NA) +
geom_text(aes(y = 0, label = paste(species_first, " ")), vjust = 0.2, hjust = 1) +
geom_text(aes(y=n, label = n, hjust=0)) +
coord_flip(clip = "off", expand = FALSE) +
scale_y_continuous(labels = scales::comma) +
scale_x_reverse() +
guides(color = FALSE, fill = FALSE) +
theme(axis.line=element_blank(),
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
legend.position="none",
panel.background=element_blank(),
panel.border=element_blank(),
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),
panel.grid.major.x = element_line( size=.1, color="grey" ),
panel.grid.minor.x = element_line( size=.1, color="grey" ),
plot.title=element_text(size=25, hjust=0.5, face="bold", colour="grey", vjust=-1),
plot.subtitle=element_text(size=18, hjust=0.5, face="italic", color="grey"),
plot.caption =element_text(size=8, hjust=0.5, face="italic", color="grey"),
plot.background=element_blank(),
plot.margin = margin(2,2, 2, 4, "cm"))anim = staticplot + transition_states(year, transition_length = 4, state_length = 1) +
view_follow(fixed_x = TRUE) +
labs(title = 'Total Number of Planted Trees per Year: {closest_state}',
subtitle = "Top 10 Species")For gif
animate(anim, 200, fps = 2, width = 1200, height = 1000,
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## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
For Video
# For MP4
for_mp4 <- animate(anim, 200, fps = 5, width = 1200, height = 1000, renderer = av_renderer()) ## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?
## Warning: Position guide is perpendicular to the intended axis. Did you mean to
## specify a different guide `position`?anim_save("animation.mp4", animation = for_mp4 )Alternative: cumulative total of top 5 species over time
find out which are the top 5 most planted species over entire time period. ‘Trees’ category will be omitted as it tells us nothing about species
df_agg <- aggregate(df_trees_hasdate_tidy$n, by=list(df_trees_hasdate_tidy$species_first), FUN='sum')
df_agg %>%
arrange(desc(x)) %>%
top_n(n=6)## Selecting by x## Group.1 x
## 1 Tree(s) 10066
## 2 Prunus 6393
## 3 Tristaniopsis 4652
## 4 Lophostemon 4100
## 5 Magnolia 3773
## 6 Arbutus 3475create df to be used for cumulative summation
df_top5 <- df_trees_hasdate_tidy %>%
filter(species_first == 'Prunus' | species_first == 'Tristaniopsis' | species_first == 'Lophostemon' | species_first == 'Magnolia' | species_first =='Arbutus')Calculate the cumulative summation for each species.
df_top5_cumsum <- df_top5 %>%
group_by(species_first) %>%
mutate(csum = cumsum(n))#install.packages('transformr')
library('transformr')Save the data type of year column as Date
df_top5_cumsum$year <- lubridate::ymd(df_top5_cumsum$year, truncated = 2L)Create the static plot
species_cumsum <- ggplot(df_top5_cumsum, aes(x=year,y=csum, group=species_first, col=factor(species_first))) + geom_line() + scale_color_manual(values = c('#e41a1c', '#377eb8', '#4daf4a', '#984ea3', '#ff7f00')) + theme_minimal() Create the animated plot with transition
anim2 <- species_cumsum + transition_reveal(year) + view_follow(fixed_x = TRUE) +
labs(title = 'Cumulative Total of Top 5 Species over Time', x = 'Year', y = 'Cumulative Sum')Animated graph (gif version):
animate(anim2, 200, fps = 3, width = 1200, height = 1000,
renderer = gifski_renderer("gganim2.gif"))
#Analysis 2:
map of recommended species per (https://sfenvironment.org/sites/default/files/fliers/files/sf_tree_guide.pdf) :
recommended_sp <- c(' Japanese Blueberry Tree', ' Flaxleaf Paperbark', ' Red Flowering Gum', ' Flowering Cherry',
' Little Gem Magnolia', ' Southern Magnolia', ' Weeping Bottlebrush', ' Hybrid Strawberry Tree',
' Primrose Tree', ' Brisbane Box', ' Mediterranean Fan Palm', ' Fruitless Olive', ' Chilean Soapbark',
" Small-leaf Tristania 'Elegant'", ' Chinese Pistache', ' Trident Maple', ' Chinese Elm', ' Cork Oak',
' Ginkgo: Autumn Gold', ' Fairmont Ginkgo', ' Ginkgo: Saratoga', ' Autumn Sentinel Ginkgo'
)unique(df_trees[grep(df_trees$species_nor, pattern = "Ginkgo", ignore.case = TRUE), 'species'])## [1] Ginkgo biloba 'Autumn Gold' :: Ginkgo: Autumn Gold
## [2] Ginkgo biloba 'Fairmont' :: Fairmont Ginkgo
## [3] Ginkgo biloba 'Saratoga' :: Ginkgo: Saratoga
## [4] Ginkgo biloba 'Autumn Sentinel' :: Autumn Sentinel Ginkgo
## 571 Levels: :: ... Ziziphus jujuba :: Jujubedf_trees$species_nor <- as.factor(df_trees$species_nor)df_trees_filtered <- df_trees %>%
filter(species_nor %in% recommended_sp)unique(df_trees_filtered$species_nor)## [1] Southern Magnolia Red Flowering Gum
## [3] Hybrid Strawberry Tree Chinese Elm
## [5] Brisbane Box Weeping Bottlebrush
## [7] Little Gem Magnolia Small-leaf Tristania 'Elegant'
## [9] Chinese Pistache Fruitless Olive
## [11] Japanese Blueberry Tree Trident Maple
## [13] Flaxleaf Paperbark Primrose Tree
## [15] Ginkgo: Autumn Gold Chilean Soapbark
## [17] Cork Oak Mediterranean Fan Palm
## [19] Fairmont Ginkgo Ginkgo: Saratoga
## [21] Autumn Sentinel Ginkgo Flowering Cherry
## 551 Levels: 'Akebono' Cherry Acacia Spp ... YuccaGet the coordinates of the whole dataset
df_trees_filtered %>%
summarise(max_lon = max(longitude, na.rm=TRUE), min_lon = min(longitude, na.rm=TRUE),
max_lat = max(latitude, na.rm=TRUE), min_lat = min(latitude, na.rm=TRUE))## max_lon min_lon max_lat min_lat
## 1 -122.3692 -138.2839 47.27022 37.70793register_google('AIzaSyB2pTXikWRKM3XgN4WC-p-Fu2mOs8fZK88')san_francisco = c(left=-122.7, bottom = 37.7, right = -122.3, top = 37.85)
smap <- get_map(san_francisco, maptype = 'hybrid') %>% #get_stamenmap(san_francisco, maptype = 'watercolor')
ggmap()## Source : http://tile.stamen.com/terrain/12/651/1582.png## Source : http://tile.stamen.com/terrain/12/652/1582.png## Source : http://tile.stamen.com/terrain/12/653/1582.png## Source : http://tile.stamen.com/terrain/12/654/1582.png## Source : http://tile.stamen.com/terrain/12/655/1582.png## Source : http://tile.stamen.com/terrain/12/656/1582.png## Source : http://tile.stamen.com/terrain/12/651/1583.png## Source : http://tile.stamen.com/terrain/12/652/1583.png## Source : http://tile.stamen.com/terrain/12/653/1583.png## Source : http://tile.stamen.com/terrain/12/654/1583.png## Source : http://tile.stamen.com/terrain/12/655/1583.png## Source : http://tile.stamen.com/terrain/12/656/1583.png## Source : http://tile.stamen.com/terrain/12/651/1584.png## Source : http://tile.stamen.com/terrain/12/652/1584.png## Source : http://tile.stamen.com/terrain/12/653/1584.png## Source : http://tile.stamen.com/terrain/12/654/1584.png## Source : http://tile.stamen.com/terrain/12/655/1584.png## Source : http://tile.stamen.com/terrain/12/656/1584.pngsmap + geom_point(data = df_trees_filtered, aes(x=longitude, y = latitude, col = species_nor)) #+ scale_color_manual(values = c('#e41a1c', '#377eb8', '#4daf4a', '#984ea3', '#ff7f00'))## Warning: Removed 401 rows containing missing values (geom_point).
Create map with leaflet() package
## for all species
## will be added a color for each species.
#map center
mlong = -122.4446
mlat = 37.72
pal <- colorFactor('viridis', domain = recommended_sp)
leaflet(data = df_trees_filtered,
width = '100%',
height = 800,
options = leafletOptions(minZoom = 9, maxZoom = 18)) %>%
addTiles() %>%
setView(lng = mlong, lat = mlat, zoom = 12) %>%
addCircleMarkers(lng = df_trees_filtered$longitude,
lat = df_trees_filtered$latitude,
color = ~pal(df_trees_filtered$species_nor),
popup = df_trees_filtered$species_nor,
label = df_trees_filtered$species_nor,
radius = 4) %>%
addLayersControl(overlayGroups = df_trees_filtered$species_nor) ## add layers control## Warning in validateCoords(lng, lat, funcName): Data contains 319 rows with
## either missing or invalid lat/lon values and will be ignoredbut map is too chaotic give large number of species…sooo Shiny to the rescue:
Create a shiny app version of the map above, with a drop down menu to look at each species at a time.
#map center
mlong = -122.4446
mlat = 37.72
pal <- colorFactor('Paired', domain = recommended_sp, reverse = TRUE)
shinyApp(
# Define the UI
ui = fluidPage(
# App title
titlePanel("Recommended Tree Species of San Francisco"),
#tabPanel(a(href='https://sfenvironment.org/sites/default/files/fliers/files/sf_tree_guide.pdf', 'Source')),
# Sidebar layout with input and output definitions
sidebarLayout(
# Sidebar panel for inputs
sidebarPanel(
# First input: Type of data
checkboxGroupInput(inputId = "species", #name of the input, widget
label = "Choose a species:",
choices = c('All Species', ' Japanese Blueberry Tree', ' Flaxleaf Paperbark', ' Red Flowering Gum',
' Flowering Cherry', ' Little Gem Magnolia', ' Southern Magnolia', ' Weeping Bottlebrush',
' Hybrid Strawberry Tree', ' Primrose Tree', ' Brisbane Box', ' Mediterranean Fan Palm',
' Fruitless Olive', ' Chilean Soapbark', " Small-leaf Tristania 'Elegant'", ' Chinese Pistache',
' Trident Maple', ' Chinese Elm', ' Cork Oak', ' Ginkgo: Autumn Gold', ' Fairmont Ginkgo',
' Ginkgo: Saratoga', ' Autumn Sentinel Ginkgo'
),
selected = ' Japanese Blueberry Tree'
)),
# Main panel for displaying outputs
mainPanel(
# Hide errors
tags$style(type = "text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }"),
# Output: interactive world map
leafletOutput("map", height = 800)
)
)
),
# Define the server
server = function(input, output) {
filteredData <- reactive({
if (input$species == "All Species") {
df_trees_filtered
} else {
filter(df_trees_filtered, species_nor == input$species)
}
})
output$map <- renderLeaflet({
leaflet(filteredData(),
width = '100%',
options = leafletOptions(minZoom = 9, maxZoom = 18)) %>%
addTiles() %>%
setView(lng = mlong, lat = mlat, zoom = 12) %>%
addCircleMarkers(lng = filteredData()$longitude,
lat = filteredData()$latitude,
popup = filteredData()$species_nor,
color = ~pal(filteredData()$species_nor),
label = ~species_nor,
radius = 4,
fillOpacity = 0.99)
})
}
)Shiny applications not supported in static R Markdown documents
#Analysis 3: - another map with rare (n=1) species
create list of rare species with name matching original df_trees
species_rare <- df_trees_species_count%>%
filter(n == 1) %>%
separate(species, sep = "::", remove = FALSE, into = c('species_lat', 'species_nor'))use list of rare species to subset original df_trees and also group them by common first name (i.e family name) to reduce species number
df_trees_rare <- df_trees %>%
filter(species_nor %in% species_rare$species_nor) %>%
separate(species_lat, sep = " ", remove = FALSE, into = c('species_first', 'species_second', 'species_third'))## Warning: Expected 3 pieces. Additional pieces discarded in 18 rows [5, 7, 8, 9,
## 10, 11, 12, 14, 16, 17, 25, 27, 28, 43, 58, 61, 62, 67].plot map with ggmap
smap + geom_point(data = df_trees_rare, aes(x=longitude, y = latitude, col = species_first))
plot map using leaflet, to create a hover-over dot pop up with species name, given not enough colors to differentiate so many species
#map center
mlong = -122.4446
mlat = 37.72
rare_species_vec <- unique(df_trees_rare$species_lat)
pal <- colorFactor('Paired', domain = rare_species_vec)
leaflet(data = df_trees_rare,
width = '100%', height = 800,
options = leafletOptions(minZoom = 9, maxZoom = 18)) %>%
addTiles() %>%
setView(lng = mlong, lat = mlat, zoom = 12) %>%
addCircleMarkers(lng = df_trees_rare$longitude,
lat = df_trees_rare$latitude,
popup = df_trees_rare$species_lat,
label = df_trees_rare$species_lat,
radius = 4,
fillOpacity = .5)